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Google recently rolled out Wave to the Google Apps users. googsystray currently doesn't all Apps accounts to check the Wave box with the message of "This service does not support Google Apps accounts."
I was just recently informed of this. I've already done a freeze for 1.2, which should be out soon, so look for this (and a bunch of other fixes to Wave) in 1.3, which hopefully shouldn't take the 4 months that 1.2 has.
Removing Wave support as of 1.2.1. It was kinda broken already to begin with, and with Google's announcement of discontinuing Wave, I'm closing all Wave-related bugs and feature requests.